The Tokugawa Shogunate fell in part by simply getting to be too old and in part because of contact with the outside world.
The Tokugawa Shogunate began in the early 1600s. By the mid-1800s, the system was not working so well any more. The Japanese system had, like European feudal systems, tried to keep all the power in the hands of elites whose power and wealth came from their ownership of land. But this sort of system became less and less useful as the country became more commercialized and merchants came to have more and more wealth and power. The system was also weakened militarily as daimyo became more powerful relative to the shogun.
All of this came to a head after Commodore Perry "opened" Japan. At that point, it became clear that the previous system had resulted in a Japan that was unable to protect itself against foreign powers. There was a clear need for change. The change was brought about by a rebellion that was led by the provinces of Satsuma, Tosa, and Choshu. All of these were Southern provinces most impacted by the coming of Westerners and who saw most clearly the need for change. They called themselves an imperial army, defeated the shogunate, and gave power to the Meiji Emperor.